Welcome & Workshop Overview
Words of value to let folks know what we are up to 1. eDNA Basics -
We will cover the following things that will be a quick line so folks
can get the gist 2. Experimental Design: Preparation & Sampling - We
will take a dive into how to set ourselves up for success 3. Sample
Processing & Analysis - We will enjoy a high level overview of the
decisions, stages, and analysis options based on the decisions we made
in part 1
Intro to me and my background
I have done some cool things and I will have a neat picture here to
show what i mean!
> This is my figure caption because it looks cool with the little
line next to it
Background
Introduction
Environmental DNA (eDNA) is revolutionizing biodiversity monitoring
and ecological research. In this session, we explore what eDNA is, how
it works, and its expanding role in conservation, research, and museum
science.
What is eDNA?
Environmental DNA (eDNA) refers to genetic material obtained directly
from environmental samples — such as water, soil, air, or snow — without
the need to isolate target organisms.
eDNA includes: - Shed skin, mucus, feces - Decomposed tissue -
Gametes - Extracellular fragments floating in the environment
A Brief History of eDNA
Early Foundations (Pre-2008)
- Ancient DNA work from sediments and permafrost (e.g., Willerslev,
Pääbo).
- Soil microbial ecology laid the foundation for extracting DNA from
complex environments.
Pioneering Detection (2008–2012)
- Ficetola et al. (2008): Detected bullfrog DNA from pond
water.
- Established proof-of-concept: presence without physical
capture.
High-Throughput Era (2012–2016)
- Introduction of metabarcoding and next-gen sequencing.
- Shift from single-species qPCR to community-level assessments.
- Use of genetic markers like COI, 16S, 18S.
Widening the Lens (2016–2020)
- Applications expanded beyond water: air, soil, snow, even spider
webs.
- eDNA began to inform policy (e.g., endangered species
detection).
- Museums began exploring ethanol and substrate eDNA.
Current Trends (2020–Present)
- Portable sequencing (e.g., Nanopore) for field applications.
- Use in restoration, climate resilience, and community science.
- Challenges include interpretation, persistence, and contamination
control.
Why Use eDNA?
- Non-invasive: No need to catch or disturb
organisms.
- Broad spectrum: Can detect many taxa from a single
sample.
- Cost-effective: Reduces field time, increases
resolution.
- Powerful in challenging environments: Deep sea,
wetlands, sediment cores.
Applications of eDNA
Ecology & Conservation
- Community biodiversity surveys
- Invasive species detection
- Rare/endangered species monitoring
Museum and Archive Contexts
- Ethanol from preserved specimens
- Substrate sampling (e.g., drawer dust, case sediment)
- Linking DNA to voucher specimens
Other Fields
- Pathogen surveillance (e.g., wastewater SARS-CoV-2 detection)
- Airborne eDNA for terrestrial surveys
- Sediment cores for historical biodiversity analysis
Core Concepts
Key Marker Genes
- COI – animals
- 16S – bacteria & archaea
- 18S – eukaryotes
- ITS – fungi
ASVs vs. OTUs
- ASVs (Amplicon Sequence Variants): Exact sequence
identification
- OTUs (Operational Taxonomic Units): Clustered
sequences by similarity
Limitations and Considerations
- eDNA doesn’t always indicate live presence
- Degradation and transport can influence spatial
accuracy
- False positives and false negatives are a concern
- Contamination control is crucial
Further Reading
- Ficetola et al. 2008 – Amphibian detection via eDNA
- Deiner et al. 2017 – Overview of aquatic eDNA
- Taberlet et al. 2012 – Origins and potentials of eDNA
- Yoccoz 2012 – Emerging roles in biodiversity monitoring
Appendix: Terminology Glossary
| eDNA |
DNA from the environment (water, soil, air) |
| Metabarcoding |
Amplifying DNA from multiple taxa at once |
| ASV |
Exact sequence from reads; higher resolution than OTU |
| OTU |
Cluster of similar sequences, usually 97% identity |
| Marker gene |
Gene used for identification (COI, 16S, 18S, ITS) |
| PCR |
Technique to amplify DNA |
| Primers |
Short DNA sequences that initiate PCR |
| Taxonomy assignment |
Matching sequences to known organisms |
| Field blank |
Control sample for detecting contamination |
| Library prep |
Preparing DNA for sequencing |
| Reference database |
Known sequences used to match taxa |
| Rarefaction |
Normalizing sequencing depth for comparison |